Femtosecond laser processing has become a critical technique for the microfabrication of hard and brittle materials, particularly in microfluidic device applications. This study focuses on the fabrication of microchannels with controllable cross-sectional profiles in silica glass, a material known for its excellent physical and chemical properties. Through a combination of experimental research and theoretical analysis, the surface generation mechanisms governing microchannel morphology are investigated, alongside the influence of various processing parameters on the surface roughness at the microchannel bottom. A comprehensive optimization method is developed to control sidewall taper and surface roughness by adjusting laser scanning paths and modes. Utilizing a composite scanning approach, the study achieves near-rectangular microchannels with average sidewall taper angles below 5° and surface roughness (Sa) of 2.53 μm. These results provide a new strategy for precise control of microchannel morphology in silica glass, offering significant potential to enhance the efficiency and precision of microfluidic device fabrication, with broad applications in both industrial and research settings.